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NOD-like receptor

NOD-like receptors (NLRs) are a family of cytosolic pattern recognition receptors essential to the innate immune system, functioning as sensors that detect intracellular pathogen-associated molecular patterns (PAMPs) from microbes and damage-associated molecular patterns (DAMPs) from host cell stress or damage.^[1] These receptors, numbering 23 in humans and 34 in mice, enable rapid immune responses by recognizing diverse ligands such as bacterial peptidoglycans (e.g., γ-D-glutamyl-meso-diaminopimelic acid for NOD1 and muramyl dipeptide for NOD2), toxins, viral components, and endogenous signals like ATP or uric acid crystals.^[2] Upon ligand binding, NLRs undergo conformational changes that promote self-oligomerization, forming multiprotein complexes known as inflammasomes or nodosomes to initiate downstream signaling.^[1] Structurally, NLRs share a conserved tripartite architecture: an N-terminal effector domain (variably a pyrin domain [PYD], caspase activation and recruitment domain [CARD], acidic domain, baculovirus inhibitor of apoptosis repeat [BIR], or unknown in NLRX1), a central nucleotide-binding oligomerization domain (NOD or NACHT) that facilitates ATP-dependent oligomerization, and a C-terminal leucine-rich repeat (LRR) domain responsible for ligand sensing and autoregulation.^[2] Exceptions include NLRP1, which has a C-terminal CARD instead of an N-terminal one, and NLRP10, lacking LRRs.^[1] Based on the N-terminal domain, NLRs are classified into subfamilies: NLRA (e.g., CIITA, involved in MHC class II expression), NLRB (e.g., NAIP, neuronal apoptosis inhibitor protein), NLRC (e.g., NOD1/NLRC1 and NOD2/NLRC2 for peptidoglycan sensing, NLRC4 for bacterial flagellin and type III secretion systems), NLRP (e.g., NLRP3, the most studied for broad DAMP/PAMP detection), and NLRX (e.g., NLRX1 for mitochondrial antiviral signaling).^[1] Evolutionarily, NLRs trace back to plant resistance (R) genes, with expansions through gene duplication in vertebrates, reflecting adaptations to diverse threats.^[2] In terms of function, activated NLRs trigger multiple pathways: NLRC subfamily members like NOD1 and NOD2 activate nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling to induce proinflammatory cytokines (e.g., TNF-α, IL-6) and antimicrobial peptides, while also promoting autophagy against intracellular bacteria.^[2] NLRP and NLRC4 inflammasomes recruit adaptor protein ASC and procaspase-1, leading to caspase-1 autoactivation, which cleaves pro-IL-1β and pro-IL-18 into mature forms and gasdermin D for pyroptotic cell death, a lytic process that amplifies inflammation.^[1] Some NLRs, such as NLRP3, integrate multiple signals (e.g., potassium efflux, reactive oxygen species, lysosomal damage) via regulators like NEK7, and can form broader complexes like PANoptosomes involving ZBP1 or AIM2 to drive PANoptosis (pyroptosis, apoptosis, necroptosis).^[1] Beyond immunity, NLRs influence gut microbiota homeostasis (e.g., NLRP6 in mucus production) and adaptive responses (e.g., NLRC5 in MHC class I expression).^[2] Dysregulation of NLRs contributes to a spectrum of diseases, underscoring their therapeutic potential. Gain-of-function mutations in NLRP3 cause cryopyrin-associated periodic syndromes (CAPS), including familial cold autoinflammatory syndrome and Muckle-Wells syndrome, characterized by excessive IL-1β-driven inflammation.^[1] Loss-of-function variants in NOD2 are strongly associated with Crohn's disease, impairing bacterial clearance and leading to chronic intestinal inflammation.^[2] Other links include NLRP1 in skin disorders like atopic dermatitis, NLRC4 in autoinflammatory syndromes with macrophage activation, and NLRP3 hyperactivity in gout, type 2 diabetes, atherosclerosis, and neurodegenerative diseases like Alzheimer's via chronic sterile inflammation.^[1] In infections, NLR deficiencies heighten susceptibility to pathogens like Salmonella or influenza, while overactivation can exacerbate sepsis or COVID-19 severity.^[2] Ongoing research targets NLR pathways with inhibitors (e.g., MCC950 for NLRP3) to balance immunity and inflammation.^[1]

Overview

Definition and Discovery

NOD-like receptors (NLRs), also known as nucleotide-binding oligomerization domain-like receptors, constitute a family of intracellular pattern recognition receptors (PRRs) that detect pathogen-associated molecular patterns (PAMPs) from invading microbes and damage-associated molecular patterns (DAMPs) from host cells under stress or damage, thereby initiating innate immune responses such as inflammation and cell death pathways.^[3] These receptors are primarily expressed in immune cells like macrophages and dendritic cells but also in epithelial and other non-immune cells, enabling surveillance of the cytosolic compartment for threats that evade extracellular detection.^[4] The discovery of NLRs emerged from early 2000s research on innate immunity, building on the identification of related proteins in the apoptotic machinery. NOD1, the first member, was cloned and characterized in 1999 by Inohara et al. as a protein with a caspase recruitment domain (CARD), nucleotide-binding domain (NBD), and leucine-rich repeats (LRRs), capable of activating nuclear factor-kappa B (NF-κB) and caspase-9 in response to intracellular signals.^[5] This was followed by functional studies in 2000 demonstrating NOD1's role in NF-κB activation through an induced proximity model involving the kinase RICK.^[6] NOD2 was identified shortly after in 2001 through positional cloning efforts, with Ogura et al. describing it as a susceptibility gene for Crohn's disease via frameshift mutations that impair its function, and Hugot et al. confirming leucine-rich repeat variants associated with the inflammatory bowel disorder.^[7] These findings established NLRs as key sensors in host defense and linked their dysregulation to human disease. NLRs exhibit evolutionary conservation across eukaryotes, with foundational homologs in plants represented by nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins that mediate resistance to pathogens through similar domain architectures for ligand sensing and signaling.^[8] In vertebrates, the NLR family expanded to 23 members in humans and 34 in mice, reflecting adaptations in complex immune systems.^[1] This conservation underscores NLRs' ancient role in cytosolic immunity, predating the divergence of plant and animal lineages.

Biological Significance

NOD-like receptors (NLRs) serve as critical intracellular sensors in the innate immune system, detecting microbial patterns and cellular stress signals to initiate protective responses against pathogens. They play essential roles in host defense by recognizing components from bacteria, viruses, and other invaders, thereby triggering cytokine production and antimicrobial mechanisms that bolster immune homeostasis. For instance, NLRs such as NOD1 and NOD2 detect bacterial peptidoglycan derivatives, enabling rapid responses to intracellular infections.^[4] Additionally, certain NLRs respond to sterile injury signals, such as damage-associated molecular patterns (DAMPs), helping to resolve tissue damage and prevent excessive inflammation.^[9] Beyond innate immunity, NLRs bridge the gap to adaptive immunity by modulating antigen presentation and T-cell priming, for example through the regulation of major histocompatibility complex (MHC) class I and II expression via NLRs like NLRC5 and CIITA. They also regulate key processes including inflammation, autophagy, and programmed cell death; inflammasome-forming NLRs activate caspase-1 to promote pyroptosis, an inflammatory form of cell death that eliminates infected cells, while others like NLRX1 induce autophagy to clear intracellular threats. These functions collectively maintain immune balance, with NLRs integrating signals to fine-tune responses and prevent chronic activation.^[10]^[11] NLRs are widely expressed across cell types, including professional immune cells such as macrophages and dendritic cells, as well as non-immune tissues like epithelial barriers and neurons, allowing broad surveillance of potential threats. This ubiquitous expression underscores their significance in systemic immune homeostasis and host protection. Dysregulation of NLR signaling, often through genetic variations, disrupts these balances and contributes to autoimmunity by promoting unchecked inflammation. Subfamily-specific roles, such as those of the NLRP and NLRC subfamilies in inflammasome assembly, further highlight their diverse contributions to immunity.^[4]^[9]

Molecular Structure

Core Domains

NOD-like receptors (NLRs) exhibit a conserved tripartite architecture that enables their role in innate immune sensing, consisting of an N-terminal effector domain, a central NACHT domain, and typically a C-terminal leucine-rich repeat (LRR) domain.^[12] This modular structure, spanning approximately 800–1,200 amino acids in total depending on the receptor, allows NLRs to integrate ligand detection with downstream signaling through protein oligomerization and interactions.^[13] The central NACHT domain, typically comprising 200–300 amino acids, serves as the core oligomerization module with an NTPase fold belonging to the AAA+ ATPase superfamily.^[13] This domain facilitates self-assembly of NLR monomers into higher-order complexes upon activation by hydrolyzing nucleotides like ATP, thereby acting as a molecular switch for immune response initiation.^[12] Structurally, the NACHT domain includes a nucleotide-binding subdomain, helical domain 1, winged-helix domain, and helical domain 2, which together enable the conformational changes necessary for multimer formation.^[12] At the C-terminus, the LRR domain consists of tandem leucine-rich repeats, usually 200–300 amino acids in length, that provide specificity in recognizing diverse ligands such as pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs).^[13] These repeats form a horseshoe-shaped solenoid structure that mediates ligand binding and autoregulation in the resting state, preventing premature activation.^[12] The N-terminal effector domain, varying in length but generally 50–150 amino acids, primarily functions in signal transduction by recruiting downstream adaptor or effector proteins to propagate immune responses.^[13] It regulates NLR activity through homotypic interactions, enabling the assembly of signaling platforms while also contributing to autoinhibition in the inactive conformation.^[12] Subfamily-specific variations in this domain, such as different fold types, allow functional diversity across NLRs.^[13]

Domain Variations

NOD-like receptors (NLRs) display variations in their domain composition that distinguish subfamilies and underpin their diverse roles in innate immunity, while sharing a conserved tripartite architecture consisting of an N-terminal effector domain, a central NACHT oligomerization domain, and C-terminal leucine-rich repeats (LRRs).^[14] These effector domain differences occur primarily at the N-terminus, except in select cases like NLRP1, and determine subfamily classification into NLRA (acidic activation domain), NLRB (BIR domain), NLRC (CARD domain), and NLRP (PYD domain).^[2] The NLRC subfamily is characterized by an N-terminal caspase activation and recruitment domain (CARD), which facilitates direct binding to kinases such as RIP2, as observed in NOD1 and NOD2.^[14] NLRC4 also contains this CARD domain, contributing to its distinct assembly properties within the subfamily.^[15] The canonical structure for NLRC members, including NOD1 (also known as NLRC1) and NOD2 (NLRC2), is CARD-NACHT-LRR, with the CARD positioned to mediate protein-protein interactions.^[4] In the NLRP subfamily, the N-terminal effector domain is a pyrin domain (PYD), which promotes interactions with adaptor proteins like ASC to support inflammasome assembly, as exemplified by NLRP3.^[14] The typical architecture is PYD-NACHT-LRR, with NLRP3 serving as a representative member due to its broad involvement in pathogen sensing.^[16] However, NLRP1 deviates from this pattern by incorporating a function-to-find domain (FIIND) C-terminal to the LRRs, followed by an additional CARD, resulting in a PYD-NACHT-LRR-FIIND-CARD structure.^[17] The FIIND domain in NLRP1 enables autoproteolytic cleavage between its ZU5 and UPA subdomains, a process critical for the protein's maturation and stability.^[18] Within the NLRP subfamily, NLRP10 is unique in lacking the LRR domain, resulting in a PYD-NACHT structure that may contribute to its distinct regulatory functions in immunity.^[19] The NLRB subfamily features N-terminal baculovirus inhibitor of apoptosis protein repeat (BIR) domains, unique among NLRs for their role in apoptosis regulation and present in neuronal apoptosis inhibitory proteins (NAIPs).^[14] NAIPs exhibit a BIR-NACHT-LRR architecture, with multiple BIR repeats (typically three) that distinguish them from other subfamilies and support specialized ligand interactions.^[15] These domain variations across subfamilies allow NLRs to adapt their effector functions while maintaining LRR-mediated ligand recognition.^[2] The NLRX subfamily, represented by NLRX1, exhibits a non-canonical structure lacking both a recognizable N-terminal effector domain (PYD, CARD, etc.) and LRRs; instead, it features a central NACHT domain flanked by unique N- and C-terminal regions that facilitate mitochondrial localization and antiviral signaling.^[20]

Classification and Nomenclature

Subfamily Categories

The NOD-like receptor (NLR) family in humans comprises 22 genes, categorized into five subfamilies based on the N-terminal effector domain architecture, with some members as pseudogenes or having limited functionality.^[21]^[22] This classification reflects structural similarities and shared evolutionary origins.^[13] The NLRA subfamily contains one member, CIITA (class II transactivator), featuring an acidic transactivating domain and involved in regulating MHC class II expression. The NLRB subfamily, also known as NAIP (NLR family apoptosis inhibitory protein), includes one functional member in humans with baculoviral IAP repeat (BIR) domains; it senses bacterial effectors. Mice have seven NAIP paralogs (Naip1-7).^[23] The NLRC subfamily consists of five members (NLRC1 to NLRC5), characterized by a caspase recruitment domain (CARD) and roles in NF-κB activation and inflammasome signaling. These include NLRC1 (also known as NOD1) and NLRC2 (NOD2), the first discovered NLRs involved in peptidoglycan sensing; NLRC3 (also called NOD3), NLRC4 (also IPAF, detects bacterial flagellin and type III secretion systems), and NLRC5 (NOD4, regulates MHC class I expression).^[14]^[2] The NLRP subfamily has 14 members (NLRP1 to NLRP14), defined by an N-terminal PYRIN (PYD) domain important for inflammasome assembly. Examples include NLRP1 (involved in antimicrobial defenses, with unique C-terminal CARD/FIIND) and NLRP3 (senses diverse DAMPs/PAMPs in inflammation). Some, like NLRP10, lack leucine-rich repeats (LRRs) and have atypical or limited functions.^[14]^[13] The NLRX subfamily includes one member, NLRX1 (sometimes referred to as NOD5), with an unknown N-terminal domain and roles in mitochondrial antiviral signaling and regulation of reactive oxygen species.^[14] These five subfamilies account for all 22 human NLRs, highlighting their diversity in innate immune functions.^[22]

Evolutionary Relationships

NOD-like receptors (NLRs) represent an ancient family of intracellular sensors with origins tracing back to a common ancestor of plants and animals, where plant resistance (R) proteins serve as functional orthologs through shared nucleotide-binding and leucine-rich repeat architectures essential for pathogen detection.^[24] These similarities in domain organization, including the central STAND domain (NACHT in animals, NB-ARC in plants) and C-terminal LRRs, suggest convergent evolution of immune surveillance mechanisms across kingdoms, despite independent origins of the full NLR architecture in metazoans.^[25] NLR homologs are also present in fungi and protists, underscoring the broad phylogenetic distribution of this sensor class.^[26] In vertebrates, the NLR family underwent significant expansion through gene duplications, resulting in 22 functional NLR genes in humans, clustered into subfamilies NLRA, NLRB, NLRC, NLRP, and NLRX.^[21] This mammalian repertoire reflects ancient duplications predating eutherian divergence, with variations across species; for instance, teleost fish exhibit diverse NLR expansions in some lineages but fewer canonical NACHT-containing members in others compared to mammals.^[27] Key evolutionary events include the segmental duplication of the NLRP cluster in rodents following their divergence from primates approximately 90 million years ago, leading to multiple Nlrp4 paralogs in mice that are absent in humans.^[28] Conversely, primates experienced losses of certain NLR genes, such as those involved in flagellin detection, contributing to a more streamlined repertoire adapted to specific immune pressures.^[29] Sequence conservation within the NLR family is notably high in the central NACHT domain, which facilitates oligomerization and is a defining feature across vertebrates, while the LRR domains show greater variability to accommodate diverse ligand specificities.^[30] N-terminal effector domains, such as PYRIN or CARD, exhibit even more divergence, reflecting subfamily-specific adaptations, though core sensor functions remain preserved from early metazoan ancestors.^[31] This pattern of conserved core elements amid variable peripheries highlights NLRs' evolutionary flexibility in innate immunity.^[2]

Activation Mechanisms

Ligand Recognition

NOD-like receptors (NLRs) detect microbial and endogenous danger signals through their C-terminal leucine-rich repeat (LRR) domains, which serve as ligand-sensing and autoregulatory regions in these intracellular pattern recognition receptors.^[32] In specific NLRs like NOD1 and NOD2, the LRR domains directly bind pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs), while others such as NLRP3 respond indirectly to diverse signals that induce cellular perturbations.^[13] These LRR domains recognize a diverse array of PAMPs and DAMPs, initiating the innate immune response by distinguishing self from non-self or altered-self entities.^[2] Upon binding of a ligand to the LRR domain, NLRs undergo a conformational rearrangement that disrupts intramolecular auto-inhibition, thereby exposing the central NACHT oligomerization domain.^[33] This structural shift allows the NACHT domain to become accessible for self-association, marking the critical transition from a resting to an active state without directly involving downstream signaling at this stage.^[32] The precision of this mechanism ensures that only relevant threats trigger NLR engagement, maintaining cellular homeostasis. NLR ligands encompass both microbial and endogenous molecules, with representative examples including bacterial peptidoglycan fragments as PAMPs that directly bind to LRR domains in select NLRs. Endogenous DAMPs, such as uric acid crystals released during cellular stress or injury, represent another major class, highlighting NLRs' role in sensing sterile inflammation.^[34] Ligand recognition can occur via direct interaction with the LRR, as seen with certain peptidoglycan motifs, or indirectly through ligand-induced perturbations like potassium efflux or lysosomal damage that propagate signals to the NLR.^[10] A key regulatory feature of NLR activation is the threshold model, which mandates integration of multiple signals to achieve full responsiveness and avert inappropriate immune activation leading to autoimmunity. Typically, this involves an initial priming signal—often from extracellular pattern recognition receptors like Toll-like receptors—that upregulates NLR expression or modifies their activity, followed by the specific PAMP or DAMP encounter to surpass the activation threshold. This multi-signal requirement fine-tunes NLR sensitivity, ensuring robust yet controlled responses to genuine threats.

Assembly Processes

Upon ligand recognition, NOD-like receptors (NLRs) undergo conformational changes that initiate assembly into higher-order oligomeric complexes, primarily mediated by the central NACHT domain, which possesses nucleotide-binding and oligomerization capabilities.^[1] This domain, consisting of nucleotide-binding (NBD), helical domain 1 (HD1), winged helix domain (WHD), and helical domain 2 (HD2) subdomains, facilitates ATP-dependent self-association, enabling the formation of wheel-like or disk-shaped structures essential for signal transduction. For inflammasome-forming NLRs, oligomerization typically involves 7-11 subunits. For instance, NLRP3 forms an open octameric wheel-like structure via NACHT domain interactions, including back-to-back, head-to-face, tail-to-tail, and face-to-face contacts, as resolved by cryo-electron microscopy (cryo-EM); this assembly requires the co-factor NEK7, which binds the NACHT-LRR interface to license oligomerization.^[35] Similarly, NLRC4 assembles into disk-like oligomers of 10-11 subunits, nucleated by NAIP sensor proteins, with each subunit undergoing a ~90° hinge rotation at the NACHT domain to propagate the complex.^[36] Non-inflammasome NLRs like NOD1 and NOD2 form distinct oligomeric platforms, often filamentous structures with adaptor proteins. These structures provide a scaffold for downstream interactions, with the number of subunits influencing the stability and efficiency of assembly.^[37] Adaptor recruitment follows oligomerization and varies by NLR architecture. NLRPs, which contain a pyrin domain (PYD), recruit the adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC) through homotypic PYD-PYD interactions; ASC then polymerizes into filaments and binds pro-caspase-1 via CARD-CARD contacts.^[1] In contrast, CARD-containing NLRs like NOD1 and NOD2 directly recruit receptor-interacting protein kinase 2 (RIP2) or caspase-1 without ASC, forming signaling platforms for NF-κB activation.^[38] Assembly distinguishes inflammasome-forming NLRs from non-inflammasome ones. Inflammasomes, such as those involving NLRP3, NLRP1, or NLRC4, culminate in visible ASC specks—dense, punctate aggregates observable by microscopy—that amplify caspase-1 activation and promote pyroptosis.^[1] Non-inflammasome NLRs, like NOD1 and NOD2, form transient oligomers without speck formation, instead prioritizing adaptor-mediated kinase signaling.^[38] This speck-based assembly in inflammasomes enhances spatial organization and signal amplification within the cytosol.^[39] Regulation of assembly is tightly controlled to prevent aberrant activation. ATP binding and hydrolysis by the NACHT domain are indispensable, driving nucleotide-dependent oligomerization while inhibitors like MCC950 disrupt this process in NLRP3.^[38] Post-translational modifications further modulate dynamics; for example, K63-linked ubiquitination stabilizes NLRP3 oligomers, whereas K48-linked ubiquitination targets them for proteasomal degradation, with deubiquitinases like BRCC3 promoting activation.^[38] Phosphorylation and other modifications, such as S-nitrosylation, also fine-tune assembly thresholds.^[1]

Signaling Pathways

NOD Subfamily Pathways

NOD1 and NOD2, the primary members of the NOD subfamily, are intracellular pattern recognition receptors that detect specific bacterial peptidoglycan-derived motifs, initiating signaling cascades critical for innate immune responses. NOD1 recognizes γ-D-glutamyl-meso-diaminopimelic acid (iE-DAP or GM-tripeptide), a component prevalent in Gram-negative and certain Gram-positive bacteria, while NOD2 senses muramyl dipeptide (MDP), a motif found in peptidoglycan from both Gram-positive and Gram-negative bacteria.^[40] Upon ligand binding to their leucine-rich repeat domains, both receptors undergo conformational changes that promote oligomerization and expose their caspase activation and recruitment domains (CARDs).^[40] These CARD domains then facilitate homotypic interactions with the CARD of the adaptor protein receptor-interacting serine/threonine-protein kinase 2 (RIP2, also known as RIPK2 or RICK), recruiting it to the receptor complex and initiating downstream signaling.^[40]^[41] The core signaling pathway downstream of NOD1 and NOD2 activation centers on RIP2-mediated ubiquitination events that drive pro-inflammatory responses. Recruited RIP2 undergoes lysine-63 (K63)-linked polyubiquitination, primarily at lysine 209 in its kinase domain, which is essential for signal propagation and independent of RIP2's kinase activity.^[41] This ubiquitination recruits the TAB1/TAB2/TAK1 complex, where transforming growth factor-β-activated kinase 1 (TAK1) phosphorylates the IκB kinase (IKK) complex, including IKKα, IKKβ, and NEMO.^[41] Activated IKK then phosphorylates the inhibitory protein IκBα, leading to its K48-linked ubiquitination, proteasomal degradation, and subsequent nuclear translocation of NF-κB dimers.^[41] In the nucleus, NF-κB binds to promoter regions of target genes, inducing expression of pro-inflammatory cytokines such as IL-6, IL-8, and TNF-α, as well as antimicrobial peptides.^[40] Additionally, the pathway activates mitogen-activated protein kinases (MAPKs), including p38 and JNK, through TAK1-mediated phosphorylation, contributing to further amplification of inflammatory gene expression and cellular responses like apoptosis in certain contexts.^[42] Beyond NF-κB and MAPK signaling, NOD1 and NOD2 promote autophagy as an alternative output to enhance bacterial clearance. Upon detecting invasive bacteria, NOD1 and NOD2 independently of RIP2 recruit autophagy-related protein 16-like 1 (ATG16L1) to the plasma membrane at sites of bacterial entry via direct interaction with bacterial peptidoglycan.^[43] This localization facilitates autophagosome formation around intracellular pathogens, targeting them for lysosomal degradation and limiting infection.^[43] Dysregulation of this process, as seen in Crohn's disease-associated variants, impairs autophagic bacterial handling.^[43] Signaling through the NOD-RIP2 axis is tightly regulated to prevent excessive inflammation, primarily through ubiquitin-modifying enzymes that provide negative feedback. The E3 ubiquitin ligase ITCH promotes K63-linked ubiquitination of RIP2, which facilitates its proteasomal degradation and attenuates sustained NF-κB and MAPK activation following NOD stimulation.^[44] Additionally, S-palmitoylation of NOD1 and NOD2 by ZDHHC5 facilitates their membrane recruitment, enhancing signaling efficiency.^[45] Similarly, the deubiquitinase CYLD removes both K63- and linear (Met1) ubiquitin chains from RIP2, limiting its oligomerization and downstream TAK1/IKK signaling to dampen pro-inflammatory outputs.^[44] These regulatory mechanisms ensure balanced immune responses, with deficiencies in ITCH or CYLD linked to hyperinflammatory states.^[46]

NLRP Subfamily Pathways

The NLRP subfamily of NOD-like receptors (NLRs) primarily functions through the formation of inflammasomes, multiprotein complexes that drive caspase-1 activation and subsequent inflammatory responses. Key members, including NLRP1, NLRP3 (also known as cryopyrin), and NLRP6, assemble ASC-dependent inflammasomes upon sensing diverse danger signals or pathogens.^[47] These proteins share a typical NLR architecture with a pyrin domain (PYD) at the N-terminus, a central NACHT oligomerization domain, and C-terminal leucine-rich repeats (LRRs) for ligand sensing, though NLRP1 uniquely features a function-to-find domain (FIIND) and CARD.^[17] Upon activation, NLRP oligomerization facilitates recruitment of the adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC) via PYD-PYD interactions, followed by ASC's CARD domain binding pro-caspase-1 to induce its dimerization and autocleavage into active caspase-1.^[48] Active caspase-1 then processes pro-interleukin-1β (IL-1β) and pro-IL-18 into their mature, secreted forms, while cleaving gasdermin D (GSDMD) to form N-terminal pores that execute pyroptosis, an inflammatory lytic cell death.^[49] NLRP3 stands out as a versatile multi-ligand sensor activated by a broad array of stimuli, including extracellular ATP (via P2X7 receptor) and bacterial ionophores like nigericin, which disrupt cellular homeostasis.^[50] Its activation follows a two-signal model: the priming signal (Signal 1), often from Toll-like receptor ligands like lipopolysaccharide (LPS), induces NF-κB-dependent transcriptional upregulation of NLRP3 and pro-IL-1β.^[51] The activation signal (Signal 2) then triggers NLRP3 oligomerization through integrated stress responses, such as potassium (K⁺) efflux, mitochondrial reactive oxygen species (ROS) production, and lysosomal membrane damage releasing cathepsins.^[52] These upstream events converge to relieve autoinhibition, enabling ASC speck formation and caspase-1 activation, with NEK7 kinase serving as a critical co-factor for NLRP3-ASC interaction. Additionally, NLRP3 activation involves deubiquitination by BRCC3 and ISGylation, while ketone bodies such as β-hydroxybutyrate suppress its activity to limit inflammation.^[53]^[45] In contrast, NLRP1 activation involves a distinct proteolytic mechanism, where pathogen-derived proteases (e.g., from Bacillus anthracis lethal factor or viral 3C-like proteases) or cellular stresses cleave NLRP1 at specific sites, leading to proteasome-mediated degradation of its N-terminal inhibitory fragment and release of the FIIND-CARD fragment for auto-processing and ASC recruitment.^[54] NLRP6, while less extensively characterized, forms ASC- and caspase-1-dependent inflammasomes in response to microbial products like lipoteichoic acid (LTA) and double-stranded RNA, following a similar two-step priming and activation process that promotes IL-1β/IL-18 release and pyroptosis, particularly in intestinal epithelial cells.^[55] Regulation across the NLRP subfamily involves post-translational modifications, such as deubiquitination for NLRP3, and inhibitors like DPP8/9 for NLRP1, ensuring tightly controlled inflammasome responses to prevent excessive inflammation.^[47]

NLRC and NAIP Subfamily Pathways

The NAIP-NLRC4 inflammasome represents a key signaling pathway in the NLRC and NAIP subfamilies, specialized for detecting bacterial components from Gram-negative pathogens. NAIP proteins, particularly NAIP2 and NAIP5 in mice (with human homologs NAIP functioning similarly), directly recognize specific bacterial motifs such as flagellin (via NAIP5/NAIP2) or type III secretion system (T3SS) needle and rod proteins (via NAIP1/NAIP2). Upon ligand binding, NAIPs undergo conformational changes that expose their nucleotide-binding (NACHT) and C-terminal CARD domains, enabling direct CARD-CARD interactions with NLRC4 (also known as IPAF). This interaction initiates a self-propagating oligomerization process, forming a wheel-like inflammasome complex that recruits the adaptor protein ASC (apoptosis-associated speck-like protein containing a CARD) through additional CARD interactions.^[36]^[56]^[57] The assembled NAIP-NLRC4 inflammasome activates caspase-1 via proximity-induced autocleavage, leading to the processing and release of pro-inflammatory cytokines IL-1β and IL-18, as well as gasdermin D-mediated pyroptosis in infected cells. Unlike some other inflammasomes, NAIP-NLRC4 activation can occur independently of NF-κB priming in certain contexts, allowing rapid responses to cytosolic bacterial invasion without prior transcriptional upregulation. This pathway is particularly effective against Gram-negative bacteria like Salmonella, Pseudomonas, and Legionella, where T3SS components serve as potent activators, highlighting its role in restricting intracellular pathogen replication.^[36]^[58]^[59] In contrast to the inflammasome-forming members, NLRC5 in the NLRC subfamily functions primarily as a transcriptional regulator rather than a sensor-adaptor. NLRC5 transactivates MHC class I genes (HLA-A, -B, -C in humans) by binding to the SXY module in their promoters and recruiting histone acetyltransferases like RFXANK and CREB-binding protein, independent of NF-κB signaling. This regulation enhances antigen presentation to CD8+ T cells, crucial for antiviral and antitumor immunity, and occurs through NLRC5's nuclear translocation and interaction with the enhanceosome complex. NLRC5 expression is induced by interferons, amplifying MHC class I surface expression without direct involvement in inflammasome assembly. Beyond transcriptional regulation, NLRC5 associates with NLRP12 in the NLRC5-PANoptosome to trigger PANoptosis, releasing cytokines and DAMPs, regulated by TLR2/TLR4 and NAD+.^[60]^[61]^[62]^[45]

NLRX Subfamily Pathways

NLRX1, the sole member of the NLRX subfamily, localizes to mitochondria and negatively regulates NF-κB and type I interferon (IFN) signaling to maintain immune homeostasis. It interacts with mitochondrial proteins like MAVS (mitochondrial antiviral-signaling protein) to dampen excessive antiviral responses and modulates reactive oxygen species (ROS) production. Upon sensing viral double-stranded DNA (e.g., from HSV-1) or bacterial components via its LRR domain, NLRX1 enhances its ATPase activity and regulates the STING-TBK1 pathway, fine-tuning type I IFN production and preventing hyperinflammation. NLRX1 also promotes autophagy and bacterial clearance in the gut, with dysregulation linked to inflammatory bowel disease and viral susceptibility.^[45]

Physiological Functions

Role in Innate Immunity

NOD-like receptors (NLRs) serve as critical intracellular sensors in the innate immune system, detecting microbial motifs and danger signals to orchestrate pathogen clearance. In defense against bacteria, NOD2 promotes xenophagy, a selective form of autophagy that targets intracellular pathogens for lysosomal degradation, thereby enhancing bacterial killing in epithelial cells and dendritic cells.^[63] Similarly, NLRP3 and NLRC4 activate inflammasomes that trigger pyroptosis, a lytic form of programmed cell death in macrophages, which releases engulfed bacteria for subsequent neutrophil-mediated destruction and limits intracellular replication of pathogens such as Salmonella typhimurium and Legionella pneumophila.^[64] These mechanisms ensure rapid elimination of invaders without relying solely on cytokine signaling.^[65] NLRs coordinate innate responses by integrating with other pattern recognition receptors and bridging to adaptive immunity. Crosstalk between NLRs and Toll-like receptors (TLRs) amplifies inflammation; for instance, TLR-induced NF-κB activation produces pro-IL-1β, which NLR inflammasomes then process into mature IL-1β via caspase-1, heightening antimicrobial activity.^[66] Additionally, NLRC5 functions as a transcriptional transactivator for MHC class I genes, upregulating expression of HLA-A, -B, -C, and associated components like TAP1 and LMP2 to enhance antigen presentation to CD8⁺ T cells, thereby linking innate detection to cytotoxic responses against infected cells.^[60] In tissue-specific contexts, NLRs tailor immunity to local threats while preserving barrier functions. In the gut epithelium, NOD2 recognizes muramyl dipeptide from commensal and pathogenic bacteria, maintaining epithelial integrity by promoting production of antimicrobial peptides and supporting intraepithelial lymphocyte survival, which reinforces the mucosal barrier against translocation.^[67] In the lungs, NLRP3 in alveolar macrophages senses viral RNA and danger signals during influenza infection, driving IL-1β release to recruit neutrophils and promote viral clearance without excessive tissue damage.^[68] NLRs also uphold intestinal homeostasis by establishing tuned activation thresholds that foster tolerance to commensal microbiota. Through regulated sensing of microbial peptidoglycan, NLRs like NOD1, NOD2, and NLRP6 modulate NF-κB signaling and inflammasome activity to prevent dysbiosis, support epithelial repair, and limit unnecessary inflammation, ensuring a balanced coexistence with the gut flora.^[69] This selective responsiveness distinguishes harmless residents from threats, sustaining immune quiescence in steady-state conditions.^[65]

Involvement in Autoinflammation

NOD-like receptors (NLRs) contribute to autoinflammation through dysregulated activation that promotes sterile inflammatory responses in the absence of infection. Gain-of-function mutations in NLRP3 lead to constitutive inflammasome assembly and excessive interleukin-1β (IL-1β) production, driving systemic autoinflammatory diseases such as cryopyrin-associated periodic syndromes (CAPS). These mutations, often located in the nucleotide-binding domain of NLRP3, lower the activation threshold, enabling spontaneous oligomerization with ASC and caspase-1 without typical danger signals, resulting in chronic low-grade inflammation characterized by fever, rash, and joint pain.^[70] Defects in NOD2 impair autophagy pathways, exacerbating autoinflammatory conditions by failing to clear damaged cellular components and maintain homeostasis. Loss-of-function mutations in NOD2, common in Crohn's disease, disrupt its interaction with ATG16L1, hindering autophagosome formation and leading to accumulation of ubiquitinated aggregates that trigger NF-κB hyperactivation and persistent cytokine release. This autophagy deficiency promotes unresolved inflammation in the intestinal mucosa, contributing to granulomatous tissue damage and chronic autoinflammatory flares.^[71] In metabolic disorders, NLRP3 senses endogenous danger signals like cholesterol crystals, linking NLR activation to sterile inflammation in atherosclerosis. Cholesterol crystals from ruptured plaques are phagocytosed by macrophages, inducing lysosomal damage and potassium efflux that prime and activate the NLRP3 inflammasome, amplifying IL-1β and IL-18 secretion to drive plaque instability and vascular inflammation. This mechanism underscores NLRP3's role in amplifying metabolic stress into chronic inflammatory cascades.^[72] Certain NLRs, such as NLRP12, act as negative regulators to resolve autoinflammation by suppressing excessive signaling. NLRP12 inhibits NF-κB and MAPK pathways in response to self-ligands, preventing overproduction of proinflammatory cytokines and maintaining immune homeostasis in tissues like the colon. Deficiency in NLRP12 leads to heightened susceptibility to autoinflammatory phenotypes, highlighting its essential role in dampening sterile inflammatory responses.^[73]

Disease Associations

Genetic Disorders

Mutations in genes encoding NOD-like receptors (NLRs) underlie several monogenic autoinflammatory disorders characterized by dysregulated innate immune responses. These conditions arise primarily from gain-of-function variants that lead to excessive inflammasome activation and cytokine production, contrasting with loss-of-function variants that confer susceptibility to complex diseases. Inheritance patterns typically follow autosomal dominant transmission for gain-of-function mutations, while susceptibility alleles exhibit more complex, often polygenic inheritance. Blau syndrome and early-onset sarcoidosis represent autoinflammatory granulomatous diseases caused by missense mutations in the NOD2 gene (also known as CARD15) that disrupt its regulatory functions, leading to dysregulated NF-κB signaling and unchecked inflammation.^[74] Blau syndrome manifests in early childhood with a triad of granulomatous dermatitis, symmetric polyarthritis, and uveitis, progressing to potential vision loss and joint deformities. It is inherited in an autosomal dominant manner due to heterozygous missense mutations, predominantly in the nucleotide-binding domain of NOD2. Early-onset sarcoidosis shares identical clinical features but occurs sporadically, often from de novo mutations in the same gene, confirming a common genetic etiology with Blau syndrome. In contrast, loss-of-function NOD2 variants, such as frameshift or nonsense mutations (e.g., L1007fs), impair bacterial sensing and are associated with increased susceptibility to Crohn's disease, a multifactorial inflammatory bowel disorder, through reduced autophagy and impaired mucosal barrier function. Gain-of-function mutations in NLRP1 are linked to rare autoinflammatory skin disorders, including NLRP1-associated autoinflammation with arthritis and dyskeratosis (NAIAD). This syndrome features chronic skin inflammation with dyskeratosis, arthritis, and elevated levels of caspase-1 and IL-18, reflecting hyperactive NLRP1 inflammasome assembly. Inheritance can be autosomal recessive, as seen in homozygous missense variants (e.g., p.Arg726Trp), or sporadic via de novo heterozygous mutations (e.g., p.Pro1214Arg). NLRP1 polymorphisms also confer susceptibility to vitiligo, an autoimmune skin depigmentation disorder, by promoting inflammasome-mediated keratinocyte death and autoantigen exposure. Cryopyrin-associated periodic syndromes (CAPS) encompass a spectrum of autoinflammatory conditions driven by gain-of-function mutations in the NLRP3 gene, encoding cryopyrin. These heterozygous variants, often in the NACHT domain, cause constitutive inflammasome activation and overproduction of IL-1β, leading to episodic fever, rash, and organ-specific inflammation. The mildest form, familial cold autoinflammatory syndrome (FCAS), presents with cold-triggered urticaria and arthralgia. Muckle-Wells syndrome involves recurrent urticaria, sensorineural deafness, and amyloidosis risk. The severe neonatal-onset multisystem inflammatory disease (NOMID) includes chronic meningitis, arthropathy, and growth failure. All CAPS subtypes follow autosomal dominant inheritance, with early IL-1 blockade therapy preventing long-term complications.

Infectious and Chronic Diseases

NOD-like receptors (NLRs) play a critical role in host defense against bacterial pathogens, with dysfunction increasing susceptibility to infections. Variants in NOD2, a key NLR involved in sensing muramyl dipeptide from bacterial peptidoglycan, have been associated with heightened risk of infections by intracellular bacteria such as Listeria monocytogenes and Mycobacterium tuberculosis. In NOD2-deficient macrophages, impaired NF-κB activation and cytokine production, including IL-12 and TNF-α, lead to reduced bacterial clearance and exacerbated disease progression in experimental models. Similarly, NOD2 polymorphisms in humans correlate with increased vulnerability to mycobacterial infections, highlighting its importance in innate immune responses at mucosal barriers.^[75]^[76]^[77] Hyperactivation of NLRC4, another NLR that detects bacterial flagellin via NAIP proteins, contributes to autoinflammatory enterocolitis during infections. Gain-of-function mutations in NLRC4 cause excessive inflammasome assembly, leading to overproduction of IL-1β and IL-18, which drive intestinal inflammation and macrophage activation syndrome in response to enteric pathogens. This manifests as severe, recurrent enterocolitis with diarrhea and tissue damage, as observed in patients with NLRC4-associated autoinflammatory disease (AID). In mouse models, NLRC4 hyperactivation in intestinal epithelial cells promotes cell expulsion and eicosanoid release, exacerbating pathology during bacterial challenges like Salmonella.^[78]^[79] In chronic diseases, NLR dysregulation links to metabolic and inflammatory conditions through persistent inflammasome activation. NLRP3 senses urate crystals in gout, triggering caspase-1-mediated IL-1β release and acute joint inflammation; this pathway is central to monosodium urate (MSU)-induced flares, as demonstrated in early studies showing NLRP3 knockout prevents MSU-driven peritonitis in mice. High glucose levels in type 2 diabetes similarly activate NLRP3 via ROS accumulation and ATP-P2X4 signaling, promoting endothelial dysfunction, insulin resistance, and β-cell pyroptosis, which worsen glycemic control and vascular complications. Some studies suggest NOD2 variants contribute to rheumatoid arthritis (RA) pathogenesis in certain populations, with polymorphisms such as rs3135500 associating with elevated RA risk and disease activity.^[80] NLRP3 exhibits dual roles in cancer, promoting tumorigenesis through IL-1β-driven angiogenesis and immune suppression while offering protection via pyroptosis in some contexts. Chronic NLRP3 activation in tumor-associated macrophages fosters a pro-tumor microenvironment by enhancing IL-1β secretion, which supports tumor growth and metastasis in models of breast and lung cancer. Conversely, NLRP3-induced pyroptosis eliminates infected or transformed cells, limiting viral oncogenesis and early tumor formation, as seen in hepatocellular carcinoma where NLRP3 deficiency accelerates progression. This ambivalence underscores NLRP3 as a therapeutic target in oncology.^[81]^[82] Therapeutic strategies targeting NLRs, particularly NLRP3 inhibitors, show promise for managing infectious and chronic diseases as of 2025. MCC950, a potent NLRP3 antagonist, demonstrated efficacy in preclinical models of gout and diabetes by blocking IL-1β release, though its clinical development was halted due to hepatotoxicity. Next-generation inhibitors, including sulfonylurea derivatives, are advancing in phase I/II trials for autoinflammatory conditions with potential extensions to chronic inflammatory diseases; for example, VTX958 from Ventyx Biosciences is in phase II trials for psoriasis and Crohn's disease, showing promising safety and efficacy profiles as of 2025.^[83]^[84] These agents inhibit NLRP3 assembly without off-target effects, offering hope for reducing infection susceptibility and ameliorating RA and metabolic syndromes.^[85]

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